Pakistan's drive against polio has been thrown into chaos after a foreign doctor was shot in the southern port city of Karachi, a day after the Taliban reiterated a ban on immunisation in the country's tribal areas.

A three-day nationwide immunisation campaign was launched on Monday but the Pakistan Taliban prohibited its administration in parts of the tribal area that borders Afghanistan, putting around 300,000 children at risk. Last year Pakistan was the country with the highest number of cases of polio.

"The Shakil Afridi factor has had an impact. Not all over Pakistan, but in certain parts, in Khyber Pakhtunkhwa, in the Pashtun community. Also in certain Pashtun communities in Karachi," said Shahnaz Wazir Ali, a senior adviser to the prime minister, who is overseeing the polio eradication campaign.

"But certainly it is receding, because we are addressing it through the communication campaign. We're telling them that this [Shakil Afridi story] is a complete misconception, don't deprive your child of a safe and healthy life because of what Shakil Afridi did."

The revelation regarding Afridi aggravated prejudice against polio drops, with many believing that they are a western conspiracy to sterilise Muslims.

Afridi had been tasked with trying to collect a DNA sample from the house where the CIA suspected the al-Qaida leader was living. A US special forces team killed Bin Laden in the house in May last year. Humanitarian aid groups across the world have condemned the use of medical cover for spying activities.

On Tuesday, gunmen sprayed a vehicle being used by a United Nations polio team in a poor, mainly Pashtun, district of Karachi. A doctor and his driver were injured.

Maryam Yunus, a spokesperson for the World Health Organisation, part of the UN, said its vehicle came under attack at around noon. "They were intercepted by men on two motorcycles, who first shot at the tyres to immobilise the vehicle, then they turned on the people in the car."

She said the doctor, Constant Dedo, from Ghana, was shot in the abdomen while the driver suffered a grazing wound to the neck. They are out of danger, she said, adding that the motive for the attack was under investigation.

Pakistan, Nigeria and Afghanistan are the only countries where polio is endemic. Pakistan aims to immunise 34 million children under the age of five in the campaign, which runs until Wednesday. So far this year, polio numbers are down on the record last year of nearly 200 new cases. The tribal zone, known formally as the Federally Administered Tribal Areas (Fata), is the most difficult region for the polio work.

Last month, two senior Pakistani Taliban commanders, who control large parts of South Waziristan and North Waziristan, both in the tribal area, issued bans on polio vaccinations. Polio work has also been stopped in districts of Khyber agency, another part of the tribal area, on the orders of another Islamist warlord.

Pakistani officials are in negotiations with militants over the ban but were not able to have it overturned ahead of the immunisation drive, so the campaign was postponed there on Monday.

In a leaflet last month, Maulvi Nazir, who holds sway over the upper half of South Waziristan, accused health workers who administer anti-polio drops of being US spies, and said the ban on the immunisations would not be lifted until missile strikes by US drone aircraft ended in the tribal areas. "In the garb of these vaccination campaigns, the US and its allies are running their spying networks in Fata which has brought death and destruction on them in the form of drone strikes," the leaflet said.

In May, Afridi was sentenced to 33 years in jail, causing a further hurdle in relations between Washington, which sees the doctor as a hero, and Islamabad, where he is viewed as a traitor for working secretly for a foreign intelligence agency.

On Thursday, Afridi's case is due to go to appeal, though it is likely to drag on. A bill will be introduced in the US Senate, by Republican Rand Paul, at the end of this week to cut off all aid to Pakistan unless it frees Afridi.